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- PDB-5kwa: complete structure of the Mycobacterium tuberculosis proteasomal ... -

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Basic information

Entry
Database: PDB / ID: 5kwa
Titlecomplete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa
ComponentsProteasome-associated ATPase
KeywordsHYDROLASE / Proteasomal ATPase
Function / homology
Function and homology information


ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / protein unfolding / cellular response to nitric oxide / proteasome complex ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / protein unfolding / cellular response to nitric oxide / proteasome complex / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / AAA ATPase forming ring-shaped complexes / Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, T. / WU, Y.J.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology2013CB911500 China
National Natural Science Foundation of China31300600 China
shenzhen science and technology innovationJCYJ20160331115853521 China
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Mycobacterium tuberculosis proteasomal ATPase Mpa has a beta-grasp domain that hinders docking with the proteasome core protease
Authors: Wu, Y. / Hu, K. / Li, D. / Bai, L. / Yang, S. / Jastrab, J.B. / Xiao, S. / Hu, Y. / Zhang, S. / Darwin, K.H. / Wang, T. / Li, H.
History
DepositionJul 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8696
Polymers109,9662
Non-polymers9034
Water37821
1
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
hetero molecules

A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
hetero molecules

A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,60718
Polymers329,8986
Non-polymers2,70912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area35100 Å2
ΔGint-193 kcal/mol
Surface area110390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.931, 111.931, 196.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / Mycobacterial proteasome ATPase


Mass: 54983.051 Da / Num. of mol.: 2 / Fragment: UNP residues 22-529
Source method: isolated from a genetically manipulated source
Details: complete proteasomal ATPase binds with ATPrS / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mpa, ERS007663_01871 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9XQP1, UniProt: P9WQN5*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 % / Description: hexagonal plate
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 100mM Tris-HCl, 20%PEG400, 200mM MgCl2, 5mM ATPrS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→43.45 Å / Num. obs: 32237 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.703 / CC1/2: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M9B, 3WHK

3m9b

3whk


Resolution: 2.9→43.45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.889 / SU B: 20.441 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 1.285 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26883 1543 4.8 %RANDOM
Rwork0.22786 ---
obs0.22974 30678 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0.75 Å20 Å2
2---1.49 Å20 Å2
3---4.84 Å2
Refinement stepCycle: 1 / Resolution: 2.9→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 56 21 7179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197278
X-RAY DIFFRACTIONr_bond_other_d0.0020.027072
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9929838
X-RAY DIFFRACTIONr_angle_other_deg0.926316282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03224.226336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.497151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2041560
X-RAY DIFFRACTIONr_chiral_restr0.0690.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3056.1173620
X-RAY DIFFRACTIONr_mcbond_other2.3036.1153619
X-RAY DIFFRACTIONr_mcangle_it3.9929.1564504
X-RAY DIFFRACTIONr_mcangle_other3.9929.1584505
X-RAY DIFFRACTIONr_scbond_it2.1926.3253658
X-RAY DIFFRACTIONr_scbond_other2.1896.3253658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8769.3925335
X-RAY DIFFRACTIONr_long_range_B_refined6.55170.6427629
X-RAY DIFFRACTIONr_long_range_B_other6.55170.6367630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 126 -
Rwork0.369 2221 -
obs--99.87 %

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